8W85

HLA-DQ2.5-gamma2 gliadin peptide in complex with DQN0385AE01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Characterizations of a neutralizing antibody broadly reactive to multiple gluten peptide:HLA-DQ2.5 complexes in the context of celiac disease.

Okura, Y.Ikawa-Teranishi, Y.Mizoroki, A.Takahashi, N.Tsushima, T.Irie, M.Harfuddin, Z.Miura-Okuda, M.Ito, S.Nakamura, G.Takesue, H.Ozono, Y.Nishihara, M.Yamada, K.Gan, S.W.Hayasaka, A.Ishii, S.Wakabayashi, T.Muraoka, M.Nagaya, N.Hino, H.Nemoto, T.Kuramochi, T.Torizawa, T.Shimada, H.Kitazawa, T.Okazaki, M.Nezu, J.Sollid, L.M.Igawa, T.

(2023) Nat Commun 14: 8502-8502

  • DOI: https://doi.org/10.1038/s41467-023-44083-4
  • Primary Citation of Related Structures:  
    8W83, 8W84, 8W85, 8W86

  • PubMed Abstract: 

    In human celiac disease (CeD) HLA-DQ2.5 presents gluten peptides to antigen-specific CD4 + T cells, thereby instigating immune activation and enteropathy. Targeting HLA-DQ2.5 with neutralizing antibody for treating CeD may be plausible, yet using pan-HLA-DQ antibody risks affecting systemic immunity, while targeting selected gluten peptide:HLA-DQ2.5 complex (pHLA-DQ2.5) may be insufficient. Here we generate a TCR-like, neutralizing antibody (DONQ52) that broadly recognizes more than twenty-five distinct gluten pHLA-DQ2.5 through rabbit immunization with multi-epitope gluten pHLA-DQ2.5 and multidimensional optimization. Structural analyses show that the proline-rich and glutamine-rich motif of gluten epitopes critical for pathogenesis is flexibly recognized by multiple tyrosine residues present in the antibody paratope, implicating the mechanisms for the broad reactivity. In HLA-DQ2.5 transgenic mice, DONQ52 demonstrates favorable pharmacokinetics with high subcutaneous bioavailability, and blocks immunity to gluten while not affecting systemic immunity. Our results thus provide a rationale for clinical testing of DONQ52 in CeD.


  • Organizational Affiliation

    Translational Research Division, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DQN0385AE01 Fab heavy chain
A, E
223Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DQN0385AE01 Fab light chain
B, F
213Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ alpha 1 chain
C, G
189Homo sapiensMutation(s): 1 
Gene Names: HLA-DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens)
Explore P01909 
Go to UniProtKB:  P01909
PHAROS:  P01909
GTEx:  ENSG00000196735 
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UniProt GroupP01909
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class II HLA-DQ-beta-1 - gamma2 gliadin peptide chimeric protein
D, H
222Homo sapiensMutation(s): 0 
UniProt
Find proteins for O19712 (Homo sapiens)
Explore O19712 
Go to UniProtKB:  O19712
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UniProt GroupO19712
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.525α = 90
b = 243.913β = 90
c = 136.081γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Structure summary